yes, as Steve mentioned, the only file you need is the .fsf file.
martin
Magno R. Guillen B. wrote:
> Thanks
>
> I will change my template and I will use one generated by the GUI and
> apply the needed changes on it. I will get back to you guy with the
> results
>
> From this I imply that the only input file in multicontrast (as well
> as in single contrast) is the design.fsf
> Thanks
>
>
> On Fri, May 28, 2010 at 7:49 AM, Martin M Monti
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> There are probably many equally good ways of doing it, but one
> relatively "safe" way is to create 1 design.fsf file form the GUI,
> rather than generating it yourself, then use a script (using
> 'sed') to modify all the important bits (e.g. subname, paths) and
> generate as many design.fsf files as subjects/runs you have.
>
> cheers
>
> Martin
>
>
> Magno R. Guillen B. wrote:
>
> Hi
> THanks for the suggestion. That is exactly what I did for one
> contracts and I replicated for the GUI generated desing.fsf
> when using 2 contrast but it did not work. The design.fsf was
> mimic exactly like the one generated by the GUI, but I found a
> difference on the design.con. I do not know if that file has
> to be generated by the user or fsl generates it automatically.
>
> Any additional suggestion?
>
> Best regards
>
>
>
> On Fri, May 28, 2010 at 1:04 AM, Stephen Smith
> <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> wrote:
>
> Hi - the easy way to find out how to create the appropriate
> design.fsf is to setup the kind of model (including contrasts)
> that you want from the GUI, and save the design.fsf - and then
> just compare that against what you're producing from your
> scripts,
> to see what they need to do differently.
>
> Cheers.
>
>
>
> On 27 May 2010, at 19:16, Magno R. Guillen B. wrote:
>
> AUTOMATING THE OPERATION OF FSL VIA SCRIPTS.
>
> Hi,
>
> I am a postdoc student at Florida International
> University; I
> have been using fsl for 3 years by now. I have tried to
> automate
> the operation of fsl via scripting. I have been
> succesful in
> automating the processing of 1 contrast model, but I
> have not
> been able to automate 2 or more contrasts.
> I have written the script to mimic the structure of the
> desing.fsf used in the operation of fsl so I can
> automate the
> processing of several datsets with one single contrast,
> but I
> have failed to aautomate 2 or more contarst design in fsl
> (modifying designTemplateFEAT.fsf ).
>
> I have executed manually fsl to process a RH-LH finger
> tapping
> paradigm to compare to the file generated by my script.
> On runing
> my script with multi contrasts, fsl performs the
> prestat part but
> it stops after a while generating the error message
> ERRORS OCURED
> DURING THE ANALYSIS.
>
> I have noticed that there is a file called: design.com
> <http://design.com>
> <http://design.com>
>
>
> Which has:
> /ContrastName1 rh
> /ContrastName2 lh
> /NumWaves 2
> /NumContrasts 2
> /PPheights 1.279210e+00 1.279210e+00
> /RequiredEffect 1.285 1.285
>
> /Matrix
> 1.000000e+00 0.000000e+00
> -1.000000e+00 0.000000e+00
>
> The same file is generated when I run my script whit the
> following content:
> /ContrastName1
> /ContrastName2
>
> I would appreciate any reference or hint to write a
> script that
> generates a model with more than 1 contrast. I thought
> it was
> only needed to write these lines on the design.fsf file
> but I was
> wrong.
>
> # Number of contrasts
> set fmri(ncon_orig) 2
> set fmri(ncon_real) 2
>
> Any help is deeply appreciated.
>
>
>
> -- Magno R. Guillen, PhD
> Office: 2220 ECE Building
> Phone: (305) 348 - 4106
> College of Engineering
> Center of Advanced Education & Technology - CATE
> Florida International University - FIU
> URL--> http://web.eng.fiu.edu/~mguil004/
> <http://web.eng.fiu.edu/%7Emguil004/>
> <http://web.eng.fiu.edu/%7Emguil004/>
>
>
> This message, including any attachments hereto, may contain
> privileged and/or confidential information and is
> intended solely
> for the attention and use of the intended addressee(s).
> If you
> are not the intended addressee, you may neither use,
> copy, nor
> deliver to anyone this message or any of its
> attachments. In such
> case, you should immediately destroy this message and its
> attachments and kindly notify the sender by reply mail.
> Unless
> made by a person with actual authority conferred by Dr.
> Guillen.
> You are urged to verify any information that is
> confusing and
> report any errors/concerns to me in writing.
>
> Este mensaje, incluyendo cualquier documento adjunto, puede
> contener información confidencial y/o privilegiada y está
> dirigida solamente para la atención y uso del o de los
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> puede
> usar, copiar o entregar a nadie este mensaje o
> cualquiera de los
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> destruir
> inmediatamente este mensaje y sus adjuntos y le
> solicitamos que
> por favor notifique por la misma vía al remitente.
> Salvo que el
> mensaje provenga de una persona con autoridad real
> conferida por
> el Dr. Guillen. Se le exhorta que verifique cualquier
> información
> confusa y me informe cualquier error o preocupación de
> forma escrita.
>
>
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> http://www.fmrib.ox.ac.uk/~steve
> <http://www.fmrib.ox.ac.uk/%7Esteve>
> <http://www.fmrib.ox.ac.uk/%7Esteve>
>
> ---------------------------------------------------------------------------
>
>
>
>
>
>
> --
> Magno R. Guillen, PhD
> Office: 2220 ECE Building
> Phone: (305) 348 - 4106
> College of Engineering
> Center of Advanced Education & Technology - CATE
> Florida International University - FIU
> URL--> http://web.eng.fiu.edu/~mguil004/
> <http://web.eng.fiu.edu/%7Emguil004/>
> <http://web.eng.fiu.edu/%7Emguil004/>
>
>
> This message, including any attachments hereto, may contain
> privileged and/or confidential information and is intended
> solely for the attention and use of the intended addressee(s).
> If you are not the intended addressee, you may neither use,
> copy, nor deliver to anyone this message or any of its
> attachments. In such case, you should immediately destroy this
> message and its attachments and kindly notify the sender by
> reply mail. Unless made by a person with actual authority
> conferred by Dr. Guillen. You are urged to verify any
> information that is confusing and report any errors/concerns
> to me in writing.
>
> Este mensaje, incluyendo cualquier documento adjunto, puede
> contener información confidencial y/o privilegiada y está
> dirigida solamente para la atención y uso del o de los
> destinatarios. Si usted no es el destinatario, usted no puede
> usar, copiar o entregar a nadie este mensaje o cualquiera de
> los documentos adjuntos. Si éste es el caso, usted debe
> destruir inmediatamente este mensaje y sus adjuntos y le
> solicitamos que por favor notifique por la misma vía al
> remitente. Salvo que el mensaje provenga de una persona con
> autoridad real conferida por el Dr. Guillen. Se le exhorta que
> verifique cualquier información confusa y me informe cualquier
> error o preocupación de forma escrita.
>
>
>
> --
>
> “Well! I’ve often seen a cat without a grin,” thought Alice, “but
> a grin without a cat! It’s the most curious thing I ever saw in my
> life!” [Lewis Carroll, Alice in Wonderland]
>
> ----------------------------------------------------------
> Martin M Monti, PhD
> MRC Cognition and Brain Sciences Unit
> 15 Chaucer Road
> Cambridge, CB2 7EF
> Off. +44 (0) 1223 273646
> http://www.mrc-cbu.cam.ac.uk/people/martin.monti/home.html
> ----------------------------------------------------------
>
>
>
>
> --
> Magno R. Guillen, PhD
> Office: 2220 ECE Building
> Phone: (305) 348 - 4106
> College of Engineering
> Center of Advanced Education & Technology - CATE
> Florida International University - FIU
> URL--> http://web.eng.fiu.edu/~mguil004/
> <http://web.eng.fiu.edu/%7Emguil004/>
>
> This message, including any attachments hereto, may contain privileged
> and/or confidential information and is intended solely for the
> attention and use of the intended addressee(s). If you are not the
> intended addressee, you may neither use, copy, nor deliver to anyone
> this message or any of its attachments. In such case, you should
> immediately destroy this message and its attachments and kindly notify
> the sender by reply mail. Unless made by a person with actual
> authority conferred by Dr. Guillen. You are urged to verify any
> information that is confusing and report any errors/concerns to me in
> writing.
>
> Este mensaje, incluyendo cualquier documento adjunto, puede contener
> información confidencial y/o privilegiada y está dirigida solamente
> para la atención y uso del o de los destinatarios. Si usted no es el
> destinatario, usted no puede usar, copiar o entregar a nadie este
> mensaje o cualquiera de los documentos adjuntos. Si éste es el caso,
> usted debe destruir inmediatamente este mensaje y sus adjuntos y le
> solicitamos que por favor notifique por la misma vía al remitente.
> Salvo que el mensaje provenga de una persona con autoridad real
> conferida por el Dr. Guillen. Se le exhorta que verifique cualquier
> información confusa y me informe cualquier error o preocupación de
> forma escrita.
>
>
--
“Well! I’ve often seen a cat without a grin,” thought Alice, “but a grin without a cat! It’s the most curious thing I ever saw in my life!”
[Lewis Carroll, Alice in Wonderland]
----------------------------------------------------------
Martin M Monti, PhD
MRC Cognition and Brain Sciences Unit
15 Chaucer Road
Cambridge, CB2 7EF
Off. +44 (0) 1223 273646
http://www.mrc-cbu.cam.ac.uk/people/martin.monti/home.html
----------------------------------------------------------
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